Related proteins: Firstly, we searched and reviewed autophagy-related scientific articles recorded by PubMed as many as possible and extracted some useful information for us. In this step, we collected 545 autophagy-related genes from 499 literatures after removing duplicates. For these genes, their molecular type, specific effects on autophagy (e.g., their increased/decreased activity will increase/decrease autophagy), species evidence and corresponding experimental references were reserved. Additionally, their pathway and disease information have also been added including canonical pathways, downstream microRNAs, proteins and chemicals, upstream proteins and chemicals, role in cell, involved disease, OMIM information, KEGG disease information. After that, we searched for the autophagy-related database and found two excellent databases: Human Autophagy Database (HADb,
Related chemicals: Similar to the protein collection process, we firstly collected 246 related chemicals from 367 literatures recorded by PubMed. For these chemicals, their molecular type, specific effects on autophagy (e.g., their increased/decreased activity will increase/decrease autophagy), species evidence and corresponding experimental references were reserved. Additionally, some pathway and disease information including target, pathway, biological description and corresponding gene name listed in aforementioned protein database. After that, we also obtained 595 new chemicals from MedChem Express, Selleck and APExBIO. Their research area, category (activator/inhibitor), in vitro/vivo test, clinical trials were reserved. For all the chemicals, some basic information was collected: IUPAC name, alternative names, canonical SMILES, molecular formula, molecular weight, solubility. Furthermore, 18 important physicochemical and ADME properties were calculated by our ADMETlab platform and chemopy package [22 (link)]: hydrogen acceptor, hydrogen donor, logD (pH = 7), pKa (pH = 7), pKb (pH = 7), druglike, logP(o/w), logS, SlogP, TPSA, loghERG, Caco-2, logBB, MDCK, logKp, logKhsa, human oral absorption, and percent human oral absorption (%). Four external links including structural and drug information were added: CAS number, PubChem CID, HMDB ID, and DrugBank ID.
Related microRNAs: In this part, we totally collected 132 autophagy related microRNAs from literatures recorded by PubMed and a noncoding RNA database, ncRDeathDB (